First, the people who run Comedy Central are cowards and hypocrites. They caved to a threat from an Islamic radical site and censored a South Park episode referring to Mohammad. Now in years past, they've been fine with South Park blasting every single other way of life in every offensive way possible. But they censored the Mohammad one. They're basically sending the signal that other religions and philosophies should be more violent if they don't want to get mocked.
Then Jon Stewart came out and gave a defense of the network (booo!) but that turned into a segment against the Islamic extremists. Stewart thanked everyone else for "taking it so well" and then played a highlight reel of the mockings Jews, Christians, Buddhists, Wiccans, atheists, etc., that the Daily Show's done over the years. He then pointed out while he may have disagreements with folks like Fox News, Jim Kramer, etc., "they are not the enemy." These Islamic extremists, he made clear, are the enemy. And then he led a choir in song to tell that group to go f*** themselves.